Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtacttccatttgacatgctgtcatcatattttaattggcaaatggtttctcatgtcataacacaaaattgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g34710.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 13
----------------gtaatgtacttccatttgacatgct------gtcatcatattttaattggcaaatggtttctcatgtcataacacaaaattgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG
| || | || | | ||| || |||||| |||| | ||| | || || | ||| | | | ||||||| ||||||||||||||||||||| || || ||||||||||||||| | ||||||||||||||||| ||||| ||||||||||| ||||||
cagaccccactcgtttgggatcctccggcactaggtctgcccccaaagttgtcatatattaaattgcatgtacttactggcgacattat-tacatttgcagAAGAACAGTTTTGAACAGTTCTGCATCAATTATGCTAATGAAAGGTTGCAACAACATTTCAATCGTCATTTATTTAAGCTTGAGCAAGAG
upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
gtaatgtacttccatttgac--atgctgtcatcatattttaattggcaaatggtttctcatgtcataacacaaaattgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG
|||||| |||| ||| | | | |||||| |||| |||| | || || ||| || || ||| | || | ||||||| ||||||||||||||||||||| ||||| ||||||||||||||| | || |||||||||||||| ||||||||||||||||| ||||||
gtaatgcacttttctttacctaaagttgtcat-atatattaaattccatatagttacttctgacattat-catatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG
upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 12
--------------------------------gta-atgtacttccatttgaca-tgctgtcatcatattttaattggcaaatggtttctcatgtcata-acacaaaatt--------gcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG
|| ||| | |||| || | | ||| ||||| | || ||| |||| ||| || | ||| |||||||||||||||||| ||||||||||| || ||||| ||||| || | |||||||| |||||||| ||||| || ||| | ||||| |||
gtatgttatattatatgacagatcttttatatgtgtgtgtgtgtgtatttatcactatccttatcctatttaattttttaaaatgtttgctctgttgtatgcggtggattttatgcatgcagAGGAACAGTTTTGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTACAACAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 12
-------------------------------gtaatgtacttcc-atttgacatgctgtcatcatatt--ttaattggcaaatggttt-------ctcatgtcat--aacacaaaattgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG
|| || || |||| | | || |||| | || || |||| ||| || ||| || | | ||||||||||||||||||| |||||||| || || ||||| ||||| || | || ||||| || ||||| ||||| || ||| | ||||| |||
gtatgtttatattaaactttatctacatctttctatatatttatgatttatctcaccatcttcatcctgtttgatattaaaatattttggctctactgatgctatgcattttatgcctgcagAGGAACAGTTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTTAATCGTCATTTATTCAAGTTAGAACAGGAG
upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
-----------------------------gtaatgtacttccatttgacatgctgtcatcat-attttaattggcaaatggtttctcatgtcataacacaaaat-----tgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG
| | || | || || |||| | || | ||| | | | ||| || | || | |||||||||||||||||||||||||||| || || ||||| ||||| || | || ||||| |||||||| ||||| || ||| | ||||| |||
gtatgtttatattaaactttatctacctctttctttatatttatgatttatctcaccatcttcatcctgtttgatattttgcctctactgatgctatgcattttatccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 14
----------------------------gta-atgtacttccatttgaca-tgctgtcatcatattttaattggcaaatggtttctcatgtcata-acacaaaatt--------gcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG
|| || || | | || | | ||| ||||| | || ||| |||| ||| || ||| |||||||||||||||||| |||||||| || || ||||| ||||| || | |||||||| |||||||| ||||| || ||| | ||||| |||
gtatgttatattatatggcagatcttttatatgcgtttttgtgtatatcactatccttatcctatttaattttttaaaatgtttgctctgttgtatgtggtggattttatgcatgcagAGGAACAGTTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGATTACAACAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 13
lower sequence: PP1S174_120V6.1 (Physcomitrella patens), 3'ss of exon 13
-----------------------------------gtaatgtacttccatttga--catgctgtcatcata-ttttaatt----ggcaaatggtt--tctcatgtcataacacaaa-------------attgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG
| | | || | | ||| | || | | ||| | ||| ||| | |||| | ||| ||| || | || |||||||| |||||||||||| ||||| || || |||||||| || |||||| | ||||||||||||||||||||| ||||||||||||| ||||||
gtgaaatcttctcatacactagaatgagattgtaagcagtttattattaattgtttcctgatctagtcaaagctttgatttctggattgatggctcttcttatggtctagcttaagcatttccctcctgattgcagAAGAACAGTTTTGAGCAGTTATGCATAAACTATGCAAACGAAAGGTTGCAACAACATTTCAATCGCCATCTGTTTAAGCTTGAGCAAGAG
upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 13
lower sequence: PP1S17_368V6.1 (Physcomitrella patens), 3'ss of exon 12
-------------gtaatgtacttccatttgacatgctgt---catcatatttta-attggca--aatggtttctcatgtcataaca--caaaattgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG
| || | | ||| ||| | | | ||| ||||| || || ||| | || | | || |||||||| ||||||||||| ||||| ||||||||||| || || ||||| | ||||||||||||||||| || ||||| |||||||| ||||||
ttattgtaggaacctgatacaagtaggttttacaaaattttcacgtcaaatttttcatctacattggaagttgttttaatcttcgctttcatgattgcagAAAAACAGTTTTGAGCAGTTGTGTATTAACTACGCAAACGAAAGATTGCAACAACATTTCAATCGTCACTTGTTCAAGCTTGAGCAAGAG
upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 13
lower sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
-----------------gtaatgtacttccatttgacatgctgtcatcatattttaattggcaaatggttt----ctcatgtcataacacaaaa-ttgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG
| || ||| | ||||| || | | | ||| ||| |||| | || | ||||||| ||||||||||| || || ||||| || ||||| ||||||||| | ||||||||||||||||| ||| |||| |||||||| ||||||
aggggtatcaggacctgaccaggt-cttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29637223|gb|CB642232.1|CB642232EST: CTGGGAGATCAATCAGCATTCTTGATATCTATGGCTTTGAATCATTCGAT AGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAA
genomic: CTGGGAGATCAATCAGCATTCTTGATATCTATGGCTTTGAATCATTCGATgtaatgtact ... aaaattgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAA
EST:
gi|300216334|gb|HO088119.1|HO088119EST: CTGGGAGATCAATCAGCATTCTTGATATCTATGGCTTTGAATCCTTCGAA AGGAACAGTTTTTAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCC
genomic: CTGGGAGATCAATCAGCATTCTTGATATCTATGGCTTTGAATCATTCGATgtaatgtact ... aaaattgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCC
EST:
gi|88741503|gb|CI765011.1|CI765011EST: CTGGGAGATCAATCAGCATTCTTGATATCTATGGCTTTGAATCATTCGAT AGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAA
genomic: CTGGGAGATCAATCAGCATTCTTGATATCTATGGCTTTGAATCATTCGATgtaatgtact ... aaaattgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
53 (upstream exon),
60 (downstream exon)
Score:
18GTGGCTTGTTGAACAAATTAACAAGTCTCTTTCAGTTGGCAAGCGTCGAACTGGGAGATCAATCAGCATTCTTGATATCTATGGCTTTGAATCATTCGATgtaatgtact ... aaaattgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcatcatattttaattggcaaatggtttctcatgtcataacacaaaattgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG
tcataac putative branch site (score: 18)
tcatattttaatt TA-rich tract